Bunyoni, whose trial opened three months ago, was prime minister from mid-2020 until September 2022 when he was fired, days after President Evariste Ndayishimiye had warned of a "coup" plot against him.
He was "sentenced to life imprisonment (on charges)... including plotting against the head of state to overthrow the constitutional regime," a judicial source told AFP on condition of anonymity.
The army general was also accused of using witchcraft to threaten the life of the head of state, undermining national security, destabilizing the economy and illegal enrichment, among other charges.
He had pleaded not guilty to all charges and said he should be acquitted because of a lack of evidence.
The court, which met in the political capital Gitega, also ordered the authorities to confiscate four houses and buildings as well as a land parcel and 14 vehicles belonging to Bunyoni, the judicial source said.
Five others in the dock including the two main co-defendants, a police colonel and a senior intelligence agent, received "sentences ranging from three years to 15 years," the source added.
The seventh defendant, a driver, was acquitted, according to the same source.
Chief Justice Emmanuel Gateretse delivered the verdict on Friday afternoon, with the court sitting in session at the prison where Bunyoni was detained.
Bunyoni was arrested in April in Burundi's economic capital Bujumbura on the eve of his 51st birthday.
A former police chief and internal security minister, Bunyoni was seen as the head of a cabal of military leaders known as "the generals" who wielded the true political power in Burundi.
A close ally of former president Pierre Nkurunziza, Bunyoni was an influential figure in the ruling CNDD-FDD party since it took power in 2005.
He had long been seen as de facto number two in the regime since a 2015 political crisis.
Ndayishimiye took power in June 2020 after Nkurunziza died of what the Burundian authorities said was heart failure amid widespread speculation he succumbed to Covid-19.
He has been hailed by the international community for slowly ending years of Burundi's isolation under Nkurunziza's chaotic and bloody rule.
But he has failed to improve a wretched human rights record and the country of 12 million people remains one of the poorest on the planet.
In 2015, Nkurunziza oversaw a crackdown on political opponents and made Burundi a global pariah amid turmoil after he launched a bid for a third term in office, in violation of a peace deal that ended a bloody civil war in 2006.